Contacts of the strand formed by residues 346 - 353 (chain A) in PDB entry 2Q0N
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 346 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A ASN 5.8 0.7 - - - +
325A ILE* 6.0 1.6 - - + -
337A ILE* 3.9 33.2 - - + -
338A ALA* 3.3 20.4 - - - +
339A THR* 4.0 13.7 - - + -
344A GLY 3.8 2.3 + - - +
345A LYS* 1.3 78.3 - - - +
347A VAL* 1.3 64.1 + - - +
382A TYR* 5.6 0.5 - - - -
397A PHE* 3.7 49.9 + - + +
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Residues in contact with VAL 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 3.9 25.4 - - + -
337A ILE* 3.3 8.1 - - - +
338A ALA* 2.9 45.4 + - + +
340A VAL* 3.6 19.1 - - + -
345A LYS* 5.8 1.1 - - + -
346A LEU* 1.3 78.8 - - - +
348A ALA* 1.3 59.6 + - - +
349A VAL* 4.3 4.0 - - + -
382A TYR* 3.9 29.6 - - + -
394A VAL* 4.0 17.3 - - + -
395A MET 3.6 8.1 - - - +
397A PHE* 4.0 8.7 - - - +
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Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A VAL* 4.7 8.7 - - + -
336A CYS 3.3 9.9 - - - +
337A ILE* 4.4 2.0 - - + +
347A VAL* 1.3 74.1 - - - +
349A VAL* 1.3 60.3 + - - +
350A LYS* 4.2 0.9 - - + -
393A VAL 4.4 0.2 - - - -
394A VAL* 3.5 3.8 - - - +
395A MET* 2.8 47.8 + - + +
396A GLU 4.0 11.7 - - - +
397A PHE* 4.1 5.4 - - + +
597A EDO 4.2 21.1 - - - +
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Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 4.0 24.5 - - + -
324A PHE* 4.2 3.6 - - + -
335A VAL* 3.5 1.5 - - - -
336A CYS* 2.8 39.2 + - + +
338A ALA* 4.2 18.6 - - + -
347A VAL* 4.3 4.7 - - + -
348A ALA* 1.3 78.7 - - - +
350A LYS* 1.3 71.7 + - - +
351A LYS* 3.4 25.0 + - - +
392A TRP* 4.0 29.4 - - + -
393A VAL 3.3 10.1 - - - +
394A VAL* 4.4 6.1 - - + -
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Residues in contact with LYS 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A THR* 6.1 0.2 - - - -
334A ILE 3.4 8.3 - - - +
335A VAL* 4.1 24.2 - - + -
348A ALA* 5.9 0.7 - - + -
349A VAL* 1.3 75.1 - - - +
351A LYS* 1.3 60.5 + - - +
352A MET* 4.2 13.8 - - + +
366A GLU* 2.8 33.4 + - - +
391A LEU 3.5 1.7 - - - +
392A TRP* 3.2 5.2 - - - -
393A VAL* 2.8 43.4 + - + +
395A MET* 4.2 25.2 - - + +
458A ASP* 3.4 36.5 + - - +
460A GLY* 4.7 2.6 - - - +
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Residues in contact with LYS 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A PHE* 4.0 18.3 - - - -
333A GLY* 3.3 4.7 - - - -
334A ILE* 2.9 49.6 + - + +
336A CYS* 2.9 42.0 - - - +
349A VAL* 3.4 18.0 + - + +
350A LYS* 1.3 75.6 - - - +
352A MET* 1.3 61.1 + - - +
390A GLU* 4.1 10.8 - - - +
391A LEU 3.4 4.3 - - - -
392A TRP* 3.7 45.8 - - + +
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Residues in contact with MET 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A THR* 3.1 47.1 - - - +
333A GLY* 4.2 1.1 - - - +
350A LYS* 4.5 17.3 - - + +
351A LYS* 1.3 77.2 - - - +
353A ASP* 1.3 62.8 + - - +
354A LEU* 3.4 1.4 + - - +
357A GLN* 3.9 1.1 - - - +
363A LEU* 3.3 24.9 - - + -
366A GLU* 3.8 18.8 - - - +
390A GLU* 3.3 5.7 - - - +
391A LEU* 2.8 76.5 + - + +
393A VAL* 4.0 16.4 - - + -
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Residues in contact with ASP 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A THR 4.5 0.8 + - - -
333A GLY* 5.6 0.4 - - - -
351A LYS 4.3 0.2 - - - -
352A MET* 1.3 70.6 - - - +
354A LEU* 1.3 65.2 + - - +
355A ARG* 2.9 64.2 + - - +
356A LYS* 3.1 33.3 + - + +
357A GLN* 2.9 25.7 + - - +
389A ASP 3.5 9.0 - - - +
390A GLU* 4.3 15.9 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il